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Small correction: BLAT is a local alignment tool Jim Kent also wrote. I think his assembler you're referring to is GigAssembler ( https://www.ncbi.nlm.nih.gov/pmc/articles/PMC31109…

The author makes a critical mistake when analyzing the BNT/Pfizer clinical trial. Over and over when discussing the results they mention calculating efficacy against "infections" u…

I recently completed my PhD in vertebrate comparative genomics so this is fun to see. The single most important factor that needs to be accounted for in analyses like these is the …

We use KT's in-memory database in a scientific computing application I work on (to store a graph 30-100GB in size accessed by 100-1000 workers). The performance is very impressive,…

To be fair, to my knowledge, LASTZ, BLAST, or BLAT don't treat IUPAC ambiguous bases (K, Y, R, etc.) in the way the OP was looking for. That's not to blame the tools, since they ha…

What proportion of bases in your query were ambiguous? If it was a fairly low percentage (~10-20%?), I think you could probably get away with using LASTZ, treating all ambiguous ba…